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- PDB-4ca9: Structure of the Nucleoplasmin-like N-terminal domain of Drosophi... -

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Basic information

Entry
Database: PDB / ID: 4ca9
TitleStructure of the Nucleoplasmin-like N-terminal domain of Drosophila FKBP39
Components39 KDA FK506-BINDING NUCLEAR PROTEIN
KeywordsISOMERASE / PROLINE ISOMERASE / NUCLEOPLASMIN / HISTONE CHAPERONE
Function / homology
Function and homology information


juvenile hormone response element binding / juvenile hormone mediated signaling pathway / macrolide binding / negative regulation of macroautophagy / FK506 binding / heterochromatin / negative regulation of autophagy / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / chromatin / nucleolus
Similarity search - Function
Peptidyl-prolyl cis-trans isomerase Fpr3/Fpr4-like / Nucleoplasmin core domain / Nucleoplasmin-like domain / Nucleoplasmin-like domain / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase / Peptidyl-prolyl cis-trans isomerase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
39 kDa FK506-binding nuclear protein
Similarity search - Component
Biological speciesDROSOPHILA MELANOGASTER (fruit fly)
MethodSOLUTION NMR / ARIA
AuthorsArtero, J. / Forsyth, T. / Callow, P. / Watson, A.A. / Zhang, W. / Laue, E.D. / Edlich-Muth, C. / Przewloka, M.
CitationJournal: J.Mol.Biol. / Year: 2015
Title: The Pentameric Nucleoplasmin Fold is Present in Drosophila Fkbp39 and a Large Number of Chromatin-Related Proteins.
Authors: Edlich-Muth, C. / Artero, J. / Callow, P. / Przewloka, M.R. / Watson, A.A. / Zhang, W. / Glover, D.M. / Debski, J. / Dadlez, M. / Round, A.R. / Trevor Forsyth, V. / Laue, E.D.
History
DepositionOct 7, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 29, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2015Group: Database references
Revision 1.2Apr 15, 2015Group: Database references
Revision 1.3May 13, 2015Group: Database references
Revision 2.0Oct 23, 2019Group: Atomic model / Data collection / Other
Category: atom_site / pdbx_database_status ...atom_site / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_database_status.status_code_cs / _pdbx_database_status.status_code_mr / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 2.1Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 2.2Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 39 KDA FK506-BINDING NUCLEAR PROTEIN
B: 39 KDA FK506-BINDING NUCLEAR PROTEIN
C: 39 KDA FK506-BINDING NUCLEAR PROTEIN
D: 39 KDA FK506-BINDING NUCLEAR PROTEIN
E: 39 KDA FK506-BINDING NUCLEAR PROTEIN


Theoretical massNumber of molelcules
Total (without water)54,1025
Polymers54,1025
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100LOWEST ERNERGY
Representative

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Components

#1: Protein
39 KDA FK506-BINDING NUCLEAR PROTEIN / PEPTIDYL-PROLYL CIS-TRANS ISOMERASE / PPIASE / ROTAMASE / DM_FKBP39


Mass: 10820.410 Da / Num. of mol.: 5 / Fragment: NUCLEOPLASMIN-LIKE, RESIDUES 3-92
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P54397, peptidylprolyl isomerase
Sequence detailsFIRST 4 RESIDUES ARE CLONING ARTIFACTS. SEQUENCE NUMBERING STARTS WITH FIRST M. A2 IS ALSO CLONING ...FIRST 4 RESIDUES ARE CLONING ARTIFACTS. SEQUENCE NUMBERING STARTS WITH FIRST M. A2 IS ALSO CLONING ARTIFACT. LAST TWO RESIDUES GS ARE CLONING ARTIFACTS.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D
121S2 CNOE
131S3 NNOE
141C13 D2O
151M0
161N15
171NOE2H15N
NMR detailsText: TWO ITERATIONS WITH 100 STRUCTURES. 20 BEST CHOSEN FOR WATER REFINEMENT. STRUCTURES CREATED BY ARIA2, RUN 62, WATER REFINEMENT.

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Sample preparation

DetailsContents: 95% WATER/5% D2O, 25MM MGCL2, 20MM SODIUM PHOSPHATE BUFFER PH 6.0
Sample conditionsIonic strength: 50 mM / pH: 6.0 / Pressure: 1.0 atm / Temperature: 298.0 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
ARIARIEPING ET ALrefinement
NMRViewANYstructure solution
CcpNmr Analysis2.2structure solution
ARIA2.1structure solution
NMRDrawANYstructure solution
CcpNmr Analysis2structure solution
DANGLE1.1structure solution
NMRPipeANYstructure solution
RefinementMethod: ARIA / Software ordinal: 1 / Details: REFINEMENT IN EXPLICIT WATER
NMR ensembleConformer selection criteria: LOWEST ERNERGY / Conformers calculated total number: 100 / Conformers submitted total number: 20

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